Nextflow workflow report

[marvelous_poitras]

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: null.

The full error message was:

Error executing process > 'NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_FILTER (Med1_VCAP_Daro_REP2)'

Caused by:
  Process `NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_FILTER (Med1_VCAP_Daro_REP2)` terminated for an unknown reason -- Likely it has been terminated by the external system

Command executed:

  samtools view \
      -F 0x004 \
      -F 0x0400 \
      -q 1 \
      -L genome.include_regions.bed \
      -b Med1_VCAP_Daro_REP2.mLb.mkD.sorted.bam \
      | bamtools filter \
          -out Med1_VCAP_Daro_REP2.mLb.noPublish.bam \
          -script bamtools_filter_se.json
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_FILTER":
      samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
      bamtools: $(echo $(bamtools --version 2>&1) | sed 's/^.*bamtools //; s/Part .*$//')
  END_VERSIONS

Command exit status:
  -

Command output:
  (empty)

Work dir:
  /input/data/work/9a/7ccc362b7ea75604b0b8924b76e1ee

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Run times
23-Jan-2024 22:57:10 - 24-Jan-2024 09:29:36 (duration: 10h 32m 26s)
  1200 succeeded  
  0 cached  
  0 ignored  
  1 failed  
Nextflow command
nextflow run /input/chipseq -profile test_full -c /experiments/experiment/chipseq/nextflow.config -c /experiments/experiment/nextflow_cws.config -c /experiments/experiment/nextflow_ceph.config
CPU-Hours
268.1 (0% failed)
Launch directory
/experiments/experiment/launch
Work directory
/input/data/work
Project directory
/input/chipseq
Script name
main.nf
Script ID
73413072355e71512cca3175a986f037
Workflow session
30b8b05f-f39e-480c-9de4-b7e399ef4d6b
Workflow profile
test_full
Nextflow version
version 23.07.0-edge, build 5875 (28-07-2023 20:27 UTC)

Resource Usage

These plots give an overview of the distribution of resource usage for each process.

CPU

Memory

Job Duration

I/O

Tasks

This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.

(tasks table omitted because the dataset is too big)